Official Government Website

Water Quality Certifications

Section 401 of the federal Clean Water Act requires state certification for any permit or license issued by a federal agency for an activity that may result in a discharge into waters of the United States (WOTUS). Water quality certifications ensure projects comply with state water quality standards and any other water quality requirements under state law.

An applicant is required to submit a Pre-Filing Meeting Request a minimum of 30 days before submitting a Water Quality Certification Request. You will receive an email receipt upon submission of the form. DEQ maintains discretion in deciding whether a pre-filing meeting is necessary. Please review the 401 Certification Guidance document for further details on the process and timeline.

Once a Section 401 certification is requested, DEQ must act within a reasonable period of time, which cannot exceed one year. The Clean Water Act Section 401(a)(1) and the final 2020 401 Rule provide that the “reasonable period of time” begins after “receipt” of a certification request (40 CFR 121.6). The final 401 2020 Rule defines “receipt” as the date that a certification request is documented as received by a certifying authority in accordance with applicable submission procedures [40 CFR 121.1(m)].

A certification request is a written document that must be signed and dated that satisfies the requirements of 40 CFR 121.5(b) or (c). To start the statutory clock, all the following components must be provided in the application:

  1. Identify the project proponent(s) and a point of contact;
  2. Identify the proposed project;
  3. Identify the applicable federal license or permit;
  4. Identify the location and nature of any potential discharge that may result from the proposed project and the location of receiving waters;
  5. Include a description of any methods and means proposed to monitor the discharge and the equipment or measures planned to treat, control, or manage the discharge;
  6. Include a list of all other federal, interstate, tribal, state, territorial, or local agency authorizations required for the proposed project, including all approvals or denials already received;
  7. Include documentation that a pre-filing meeting request was submitted to the certifying authority at least thirty days before submitting the certification request;
  8. Contain the following statement: “The project proponent hereby certifies that all information contained herein is true, accurate, and complete, to the best of my knowledge and belief”; and
  9. Contain the following statement: “The project proponent hereby requests that the certifying authority review and take action on this CWA 401 certification request within the applicable reasonable period of time.”

DEQ can waive certification (either expressly or by taking no action), deny certification, grant certification, or grant certification with conditions. If certification is granted with conditions, they become conditions of the license or permit and are enforceable.

Please download the documents below to start the Section 401 certification application process:

To facilitate the application process, please include the Joint Permit Application submitted to the Army Corps of Engineers with the 401 Certification Request Application.

This accordion will not appear on the screen

The federal Clean Water Act requires a permit to conduct water-related construction activities such as fills for development, water resource projects, and infrastructure development. The US Army Corps of Engineers is responsible for issuing dredge and fill permits in Idaho.

Section 401 Water Quality Certification Requirements for Section 404 Projects

On December 27, 2021, the United States Army Corps of Engineers (Corps) published the reissuance of forty existing Nationwide Permits (NWPs) and the issuance of one new NWP in the Federal Register (86 FR 73522). In this Federal Register notice, the Corps also announced the reissuance of thirty-two existing NWP general conditions. The forty-one NWPs and their general conditions were effective on February 25, 2022, which will expire on March 14, 2026.

On January 13, 2021, the Corps published a final rule in the Federal Register (86 FR 2744) announcing the reissuance of twelve existing NWPs and four new NWPs. In this Federal Register notice, the Corps also announced the reissuance of thirty-two existing NWP general conditions. These sixteen NWPs and their associated conditions went into effect on March 15, 2021. Thereby, replacing the previous versions that will expire on March 14, 2026.

Nationwide permits are general permits issued on a nationwide basis to streamline the authorization of activities that result in no more than minimal individual and cumulative adverse environmental effects. Many of the proposed NWPs require notification to the district engineer before commencing those activities, to ensure that the activities authorized by those NWPs cause no more than minimal individual and cumulative adverse environmental effects.

The Idaho Department of Environmental Quality (DEQ) has authority to review activities receiving Section 404 dredge and fill Nationwide Permits and issue a water quality certification (WQC) decision (Section 401(a)(1) of the Federal Water Pollution Control Act (Clean Water Act), as amended; 33 U.S.C. § 1341(a)(1); and Idaho Code §§ 39-101 et seq. and 39-3601 et seq.).

DEQ issued a final Section 401 WQC on December 4, 2020, depending on which NWP a project proponent’s activity is subject to. This document has been provided to assist with identifying what type of project activities may be subject to WQC coverage if an individual WQC may apply (Table 1).

For project activities where NWPs are partially denied or denied by DEQ, the project proponent may be required to apply for and obtain an individual certification. This link DEQ Water Quality Certifications provides further instructions on the water quality certification process and includes the pre-filing meeting request form and certification application.


2020 Coverage Under General WQC

  • 1 Aids to Navigation
  • 2 Structures in Artificial Canals
  • 4 Fish and Wildlife Harvesting, Enhancement, and Attraction Devices and Activities
  • 5 Scientific Measurement Devices
  • 6 Survey Activities
  • 7 Outfall Structures and Associated Intake Structures
  • 8 Oil and Gas Structures on the Outer Continental Shelf
  • 9 Structures in Fleeting and Anchorage Areas
  • 10 Mooring Buoys
  • 11 Temporary Recreational Structures
  • 15 U.S. Coast Guard Approved Bridges
  • 18 Minor Discharges
  • 19 Minor Dredging
  • 20 Response Operation for Oil or Hazardous Substances
  • 22 Removal of Vessels
  • 24 Indian Tribe or State Administered Section 404 Program
  • 25 Structural Discharges
  • 27 Aquatic Habitat Restoration, Establishment, and Enhancement Activities
  • 28 Modification of Existing Marinas
  • 30 Moist Soil Management of Wildlife
  • 31 Maintenance of Existing Flood Control Facilities
  • 32 Completed Enforcement Actions
  • 33 Temporary Construction, Access, and Dewatering
  • 34 Cranberry Production Activities
  • 35 Maintenance Dredging of Existing Basins
  • 36 Boat Ramps
  • 37 Emergency Watershed Protection and Rehabilitation
  • 38 Cleanup of Hazardous and Toxic Waste
  • 41 Reshaping Existing Drainage Ditches
  • 45 Repair of Uplands Damaged by Discrete Events
  • 46 Discharges in Ditches
  • 49 Coal Remaining Activities

2020 WQC

  • 48 Commercial Shellfish Mariculture Activities
  • 55 Seaweed Mariculture Activities
  • 56 Finfish Mariculture Activities

May Require an Individual WQC

(See Table 1 for denied and partially denied Nationwide Permits)
  • 3 Maintenance
  • 12 Oil or Natural Gas Pipeline Activities
  • 13 Bank Stabilization
  • 14 Linear Transportation Projects
  • 16 Return Water From Upland Contained Disposal Areas
  • 17 Hydropower Projects
  • 21 Surface Coal Mining Activities
  • 23 Approved Categorical Exclusions
  • 29 Residential Developments
  • 39 Commercial and Institutional Developments
  • 40 Agricultural Activities
  • 42 Recreational Facilities
  • 43 Stormwater Management Facilities
  • 44 Mining Activities
  • 50 Underground Coal Mining Activities
  • 51 Land-Based Renewable Energy Generation Facilities
  • 52 Water-Based Renewable Energy Generation Pilot Projects
  • 53 Removal of Low-Head Dams
  • 54 Living Shorelines
  • 57 Electric Utility Line and Telecommunications Activities1
  • 58 Utility Line Activities for Water and Other Substances2
  • 59 Water Reclamation and Reuse Facilities3

1. Listed as NWP C in 2020 General WQC
2. Listed as NWP D in 2020 General WQC
3. Listed as NWP E in 2020 General WQC

State governments authorize the Idaho Pollutant Discharge Elimination System (IPDES) permit program by the Environmental Protection Agency (EPA) to perform many permitting, administrative, and enforcement aspects. The Clean Water Act prohibits anybody from discharging “pollutants” through a “point source” into a “water of the United States” unless they have an IPDES permit. The permit will contain limits on what you can discharge, monitoring and reporting requirements, and other provisions to ensure that the discharge does not hurt water quality or people’s health.

An IPDES permit authorizes a permittee to discharge pollutants from point sources into waters of the United States in Idaho, except on tribal land.

Please visit our Permit Options web page for additional wastewater IPDES permit information.

Storm Water Regulation

DEQ requires permit coverage of storm water discharges according to applicable federal requirements. Storm water permits are typically general permits and cover storm water runoff from construction projects, industrial facilities, and municipal separate storm sewer systems (MS4). DEQ will apply regulatory criteria in IDAPA to determine which permit type to issue. Three categories of storm water discharges are covered in the IPDES Program: construction, industrial, and municipal activities.

Discharges from construction activities that disturb one or more acres, including discharges from smaller sites that are part of a common plan of development or sale, must obtain permit coverage. Construction storm water permits include requirements for erosion and sediment control, pollution prevention, and site stabilization from the Construction and Development Effluent Guidelines and Standards (40 CFR 450).

Please visit our Storm Water web page for additional permit coverage information.

The Federal Energy Regulatory Commission (FERC) is responsible for issuing licenses for the construction of new hydropower projects, relicensing existing projects, and overseeing ongoing project operations, including dam safety inspections and environmental monitoring.

Before FERC may license or relicense non-federal hydroelectric dams, a state certification is required. A company that has applied for a FERC license must request a §401 certification from DEQ. DEQ must grant or deny certification within one year of receipt of the request. If the state has not granted or denied the certification within one year of the request, certification is considered waived.

This accordion will not appear on the screen

401 Certification Lead

Tambra Phares
(208) 373-0187

ver: 3.5.1 | last updated:
Jump back to top of page button